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Table 2 Summary of the identified candidate regions and important genes of six biological phenotypes. For each phenotype, the candidate genes shown in bold were newly identified in this study while the un-bolded were reported previously

From: Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

Phenotype Chr Candidate region Type Candidate genes
Coat color 8 40,162,068-43,262,938 SNP KIT, PDGFRA, KDR
8 46,403,615-48,403,616 SNP RAPGEF2
13 44,164,643-46,177,438 SNP ADAMTS9, ATXN7
8 40,156,302-42,630,783 InDel KIT, PDGFRA, KDR
8 45,117,702-49,266,658 InDel RAPGEF2, PDGFC
13 44,164,516-46,164,570 InDel ADAMTS9, ATXN7
7 56,026,800-58,031,600 CNV CSPG4, PEAK1
8 40,222,800-42,784,000 CNV KIT, PDGFRA, KDR
Ear shape 5 29,390,982-31,646,769 SNP MSRB3, HMGA2, WIF1, LEMD3, GRIP1
7 29,294,596-31,559,390 SNP PPARD, TEAD3, TULP1, BAK1
5 29,444,163-31,682,975 InDel MSRB3, HMGA2, WIF1, LEMD3, GRIP1
7 29,303,723-31,303,724 InDel PPARD, TEAD3, TULP1, BAK1
5 28,826,400-30,866,000 CNV MSRB3, HMGA2, WIF1, LEMD3, GRIP1
Body height 7 29,294,596-31,458,775 SNP PPARD, SCUBE3, HMGA1, TEAD3, TULP1, GRM4, NUDT3, RPS10, PACSIN1, SPDEF
Body length 3 93,189,763-95,189,764 SNP PRKCE
7 29,332,971-31,332,972 SNP SCUBE3, HMGA1, GRM4, NUDT3, RPS10, PACSIN1, SPDEF
3 93,166,180-95,166,181 InDel PRKCE
Body weight 1 264,450,139-266,536,416 SNP NR6A1
2 71,760,896-74,331,103 SNP ALKBH7
4 74,356,597-76,411,729 SNP PLAG1
8 11,996,794-13,996,795 SNP LCORL
17 16,190,245-18,190,246 SNP PLCB4
X 89,361,633-91,410,843 SNP ACSL4
1 264,516,132-266,534,178 InDel NR6A1
2 71,953,098-73,953,099 InDel ALKBH7
4 74,366,801-76,390,440 InDel PLAG1
15 108,303,388-110,303,389 InDel PARD3B
X 89,368,172-91,402,512 InDel ACSL4
Gradient zone 5 92,898,692-94,907,622 SNP KITLG
8 40,286,000-42,286,001 SNP KIT, PDGFRA, KDR
11 49,086,896-51,103,489 SNP EDNRB
11 61,719,059-63,719,060 SNP DCT
5 92,904,398-94,906,740 InDel KITLG
11 49,076,945-51,087,682 InDel EDNRB
  13 49,358,504-51,358,505 InDel MITF